VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 02 2013 - 02:06:50 CDT

On Tue, Apr 2, 2013 at 6:25 AM, Win Liu <mdsimulate_at_gmail.com> wrote:
> And the password is mdsimulate. Sorry forget that.

congratulations!!

with this step (creating a bogus gmail account and publishing its
password to a public mailing list) you will not only rank very high in
the running for the "moron of the month" competition, but are also
likely to violate several of usage agreement terms and - if reported
to the proper places - risk corresponding penalties.

worst of all, you helped to make life miserable for all regular users
of gmail that will have to deal with further complications when using
gmail in order to identify abuse like yours. :-(

axel.

> On Tue, Apr 2, 2013 at 12:23 AM, Win Liu <mdsimulate_at_gmail.com> wrote:
>>
>> Hi JC,
>> Sure. I create a gmail, username is benzenefftk_at_gmail.com, a folder in its
>> drive includes the bonded optimization files for benzene. Hope you can
>> figure what's wrong.
>>
>> Thanks a lot!
>> Wenhao
>>
>> On Mon, Apr 1, 2013 at 11:51 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
>>>
>>> Can you make all your files available somewhere off-list? Including the
>>> fftk logs. I wrote the bonded optimization code, so I need to be aware of
>>> weird cases like this.
>>>
>>> On Apr 1, 2013, at 11:11 PM, Win Liu wrote:
>>>
>>> > Hi VMD developers,
>>> > For a simple test to develop the forcefield with benzene molecule. In
>>> > pdb and psf, Since benzene only had one type of carbon and hydrogen, CA and
>>> > HP respectively. So the initial parameter file is
>>> > ...
>>> > BONDS
>>> > !V(bond) = Kb(b - b0)**2
>>> > !
>>> > !Kb: kcal/mole/A**2
>>> > !b0: A
>>> > !
>>> > !atom type Kb b0
>>> > !
>>> > CA HP 0.000 0.000
>>> > CA CA 0.000 0.000
>>> >
>>> > ANGLES
>>> > !
>>> > !V(angle) = Ktheta(Theta - Theta0)**2
>>> > !
>>> > !V(Urey-Bradley) = Kub(S - S0)**2
>>> > !
>>> > !Ktheta: kcal/mole/rad**2
>>> > !Theta0: degrees
>>> > !Kub: kcal/mole/A**2 (Urey-Bradley)
>>> > !S0: A
>>> > !
>>> > !atom types Ktheta Theta0 Kub S0
>>> > !
>>> > !
>>> > CA CA HP 0.000 0.000
>>> > CA CA CA 0.000 0.000
>>> >
>>> > DIHEDRALS
>>> > !
>>> > !V(dihedral) = Kchi(1 + cos(n(chi) - delta))
>>> > !
>>> > !Kchi: kcal/mole
>>> > !n: multiplicity
>>> > !delta: degrees
>>> > !
>>> > !atom types Kchi n delta
>>> > !
>>> > CA CA CA CA 0.0000 1 0.00
>>> > HP CA CA CA 0.0000 1 0.00
>>> > HP CA CA HP 0.0000 1 0.00
>>> > ...
>>> > When I am doing the bond calculation to get bond and angle parameters,
>>> > I went through the hess calculation in Gaussian and used fftk to get
>>> > BondedCalc.log file, I found the parameter, angle {CA CA HP} 0.000 0.000
>>> > Obviously, this is not right(while bond {CA CA}, bond {CA HP}, angle {CA CA
>>> > CA} all give reasonable non-zero value.) it seems that the fftk do not get
>>> > the information for this angle.
>>> > And when I l dealt with Scan torsion module, in Dihedrals to scan
>>> > table, I can only see CA CA CA CA dihedral(like 10 0 2 4, 6 8 10 0 and so
>>> > on) but no HP CA CA CA or HP CA CA HP dihedrals, but they should be
>>> > included, right? In addition, in my fftk plugin, I can not use "Edit Entry"
>>> > tab, is it the issue that need to be fixed for VMD windows version? I am
>>> > using 1.9.2 alpha.
>>> >
>>> > Sorry for long email but just to clarify my problem. Thank you in
>>> > advance!
>>> > Wenhao
>>>
>>
> 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.